tbuckley/cabot-search huggingface dataset:
Abstract 5965: B2M loss of heterozygosity in melanoma is associated with increased numbers of activated NK cells and higher expression of the NK cell inhibitory ligand, HLA-G
Authors: Mildred Galvez, Katie M. Campbell, Egmidio Medina, Antoni Ribas
Journal: Cancer Research (2023)

Abstract β2-microglobulin (B2M) is a critical subunit of antigen presenting major histocompatibility complex (MHC) class I molecules. Its genetic inactivation in tumor cells has been implicated in tumor-intrinsic immune escape and immunotherapy resistance. Currently, the impact of B2M dysregulation on tumor-immune dynamics requires furthers characterization. Using a clinical dataset of patients with melanoma treated with immune checkpoint blockade (ICB), whole-exome sequencing and bulk RNA-sequencing data from baseline tumor biopsies (n=295) were analyzed to identify somatic B2M alterations and evaluate correlative clinical outcomes, infiltrating immune cells, and gene expression patterns. No loss-of-function mutations in B2M were found; however, 50% of tumors had B2M alterations in the form of homozygous loss (n=2), loss of heterozygosity (LOH; n=56), or copy number gains (n=88). B2M LOH events were overrepresented in tumors from patients who progressed during ICB therapy compared to those who responded (34% versus 19%; Pearson chi-square test, p=0.035). Additionally, tumors with B2M LOH had lower B2M expression compared to B2M-unaltered tumors (Wilcoxon test, p=0.05). Gene set enrichment analysis revealed reduced expression of immune and inflammatory signatures in B2M-LOH tumors. Furthermore, immune cell deconvolution showed that B2M-LOH tumors had lower total immune cell counts, but greater numbers and proportions of activated natural killer (NK) cells (Wilcoxon test, numbers p=0.021, proportions p=0.032). Differential gene expression analysis revealed concordant higher expression of human leukocyte antigen G (HLA-G), an NK cell inhibitory ligand, in B2M-LOH tumors (Wilcoxon test, p=0.0035). Moreover, B2M-LOH progressive tumors had the highest median HLA-G expression and trended toward a positive correlation between increasing HLA-G expression and increasing numbers of activated NK cells (Pearson correlation, r=0.55, p=0.015). In conclusion, melanoma biopsies with B2M LOH were associated with non-response to ICB, had increased presence of activated NK cells, and demonstrated a compensatory increase in HLA-G. These results suggest that in melanoma B2M alterations may be implicated in modulating NK cell interactions and point toward HLA-G potentially playing a role in inhibiting NK cell anti-tumor activity. Citation Format: Mildred Galvez, Katie M. Campbell, Egmidio Medina, Antoni Ribas. B2M loss of heterozygosity in melanoma is associated with increased numbers of activated NK cells and higher expression of the NK cell inhibitory ligand, HLA-G [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5965.
Abstract 5958: Analysis of MDSCs as a diagnostic and therapeutic target for gastric cancer
Authors: Suguru Yamauchi, Takumi Iwasawa, Tomoaki Ito, Malcom V. Brock, Tetsu Fukunaga, Hajime Orita, Kazunori Kato
Journal: Cancer Research (2023)

Abstract Background: Gastric cancer (GC) is the second most common cancer in Japan in terms of incidence and the third most common in terms of deaths. The onset and progression of cancer are generally suppressed by the action of immune cells, which is an inflammatory response. MDSCs are thought to promote cancer progression and invasion by suppressing the function of immune cells, making them potential therapeutic and diagnostic targets. We measured MDSCs in GC patients and observed more monocyte-derived MDSCs in peripheral blood in advanced GC than in early GC. However, granulocyte-derived MDSCs showed no difference in GC progression when markers for classical MDSCs were used. We considered that granulocyte-derived MDSCs were much more abundant than monocyte-derived MDSCs in peripheral blood and were involved in cancer progression. We hypothesized that we had a new granulocyte-derived marker for advanced GC that did not show differences in classical markers, but may have different functions, and aimed to identify a novel subset that may be a therapeutic and diagnostic target. Method: For GC patients, we used heparin blood samples provided by patients who consented to Juntendo University. We analyzed the expression of various cell surface proteins against populations of CD33high, CD66bhigh, and HLA-DRlow as classical markers of MDSCs derived from granulocytes of GC patients using FACS (Melody). MDSCs were isolated by a cell sorter and used for experiments such as RNA-Seq. Novel markers and involved cytokines were quantified in plasma components by cytometric bead array. Result: The chemokine receptors CCR2, CCR5, CXCR4, and CXCR5 were highly expressed in MDSCs of advanced GC patients. The ability to suppress T-cell activation was also found to be stronger in MDSCs with advanced GC. In addition, IL-10 produced by MDSCs was also more abundant in the plasma of patients with advanced GC, as well as chemokines according to chemokine receptors. Conclusion: The high expression of chemokine receptors on MDSCs in advanced GC may indicate that chemokines produced at the cancer site facilitate the migration of MDSCs. These novel subsets of MDSCs found in advanced GC suggest that they may be new therapeutic targets. Citation Format: Suguru Yamauchi, Takumi Iwasawa, Tomoaki Ito, Malcom V. Brock, Tetsu Fukunaga, Hajime Orita, Kazunori Kato. Analysis of MDSCs as a diagnostic and therapeutic target for gastric cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5958.
Abstract 4793: A role for fibroblast derived SASP factors in the activation of non-apoptotic cell death in normal mammary epithelial cells
Authors: Lisa M. Hom, Seunghoon Sun, Jamie Campbell, Ireland Murphy, Shannon Culbert
Journal: Cancer Research (2023)

Abstract In normal tissue homeostasis, bidirectional communication between different cell types can shape numerous, biological outcomes. Fibroblasts are one cell type in constant communication with neighboring epithelial cells, and as a result, can alter various cellular parameters. Additionally, fibroblasts are prone to undergo senescence, exemplified by an irreversible cell cycle arrest, in response to a variety of stimuli. Senescent cells exhibit alterations in gene expression and are characterized by substantial changes in their secretome; termed the senescence associated secretory phenotype (SASP). The role of fibroblast derived SASP factors on normal epithelial cells is an area that remains poorly understood. Our studies have found that treatment of normal mammary epithelial cells with conditioned media from senescent fibroblasts (SASP CM) results in a robust programmed cell death. The capacity of SASP CM to cause cell death is maintained across multiple senescence-inducing stimuli. Interestingly, our data suggest that the cell death caused by SASP CM is dependent on caspase activation, but independent of canonical extrinsic or intrinsic apoptotic pathways. shRNA-mediated reduction of caspase 1 or GSDMD in normal mammary epithelial cells ameliorates the ability of the SASP CM to induce cell death, suggesting that these cells are dying by pyroptosis. Interestingly, breast cancer cells and normal mammary epithelial cells engineered to express oncogenic signals are not susceptible to this SASP CM induced cell death, suggesting that cancer cells have evolved a mechanism to evade SASP CM-mediated pyroptosis.. Taken together, our data reveal a novel relationship between the activation of senescence in stromal cells and the induction of non-apoptotic cell death in normal mammary epithelial cells. Citation Format: Lisa M. Hom, Seunghoon Sun, Jamie Campbell, Ireland Murphy, Shannon Culbert. A role for fibroblast derived SASP factors in the activation of non-apoptotic cell death in normal mammary epithelial cells. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4793.
Abstract 446: LONP1 inhibition induces mitochondrial proteotoxic stress and is cytotoxic to acute myeloid leukemia cells
Authors: Matthew Tcheng
Journal: Cancer Research (2023)

Abstract Acute myeloid leukemia (AML) is a hematological malignancy characterized by the uncontrolled proliferation of abnormal myeloid precursors that fail to fully differentiate, resulting in the accumulation of malignant leukemic cells. High rates of nuclear-encoded protein synthesis, supporting increased proliferation rates, render leukemic cells reliant on increased proteolytic systems to clear misfolded proteins. Compared to non-transformed blood cells, AML cells and stem cells exhibit a unique metabolic phenotype characterized by increased mitochondrial mass and greater reliance on oxidative metabolism for survival and proliferation. To identify novel biological vulnerabilities in the mitochondrial proteome, we analyzed the DepMap (depmap.org) for essential mitochondrial genes in AML. Through this analysis, we identified the mitochondrial protease LONP1 as essential for a subset of AML and in the top 10% of essential genes for this disease. LONP1 is a nuclear-encoded AAA+ serine protease that resides in the mitochondrial matrix and maintains the mitochondrial proteome, mainly via the clearance of misfolded, unassembled or oxidatively-damaged proteins. However, its importance and function in AML has not been previously reported. Compared to normal hematopoietic cells, LONP1 mRNA was overexpressed in AML across three publicly available datasets while LONP1 protein was increased &amp;gt;2 fold in tested AML primary samples (N=16). Using shRNA and CRISPR gRNA, LONP1 knockdown and knockout reduced the growth and viability of OCI-AML2, OCI-M2, and NB4 cells. Mechanistically, genetic knockdown or knockout of LONP1 increased levels of insoluble, aggregated mitochondrial proteins including ClpP, TUFM, and NDUFA9 as measured by immunoblotting of soluble and insoluble protein fractions as well as by the fluorescence of the protein aggregation dye PROTEOSTAT by confocal microscopy. The accumulation of insoluble mitochondrial protein aggregates through LONP1 inhibition exploits an increased reliance on chaperone and protease systems due to abnormally high protein synthesis. This novel therapeutic avenue targets a unique metabolic vulnerability to eliminate AML cells. Citation Format: Matthew Tcheng. LONP1 inhibition induces mitochondrial proteotoxic stress and is cytotoxic to acute myeloid leukemia cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 446.
Abstract 2191: Detection of actionable lung cancer fusion genes with known and novel partners from highly degraded FFPE material
Authors: Bongyong Lee, Alisha Babu, Aiguo Zhang, Michael Y. Sha
Journal: Cancer Research (2023)

Abstract Chromosomal rearrangements resulting in expression of oncogenic chimeric proteins drive tumor progression. Gene fusions are promising targets for cancer therapy in various types of cancers. Therefore, faithful detection of gene fusions is essential in precision medicine. Previously, fusions have been detected using FISH, RT-PCR and RNA-seq. Targeted sequencing provides better sensitivity as only the regions associated with the driver genes are sequenced, increasing possible coverage depth, and reducing cost. We developed a targeted RNA-based lung cancer fusion panel utilizing 5’ RACE technology to construct a NGS library for detection of fusion transcripts present in total RNA from highly degraded samples, such as blood or FFPE samples. The panel is deliberately designed to cover 64 known actionable fusion genes as well as novel gene fusions. Using an in-house fusion RNA mix comprising of 52 fusion transcripts, the panel was optimized and balanced. A total of 40 lung cancer patient FFPE samples, one 6-fusion FFPE reference sample and three fusion positive cell line samples were used for validating the panel. Limit of detection (LoD) was determined using the in-house RNA mix and normal lung tissue RNA. The minimum RNA input to detect all 52 fusion transcripts was 10-4 ng (0.1 pg) of mixture of RNAs in background of 10 ng of normal lung tissue RNA. The panel successfully detected all six fusion transcripts with 10 ng of RNA from a 6-fusion reference FFPE sample. With this confirmation, we tested clinically relevant sample types which are damaged RNAs from FFPE material. This study demonstrates the performance of our newly developed NGS fusion gene panel with clinical samples. It accommodates highly degraded RNA samples with low amounts of input. The next step would be to expand the testing to include more samples and cell-free RNAs. Citation Format: Bongyong Lee, Alisha Babu, Aiguo Zhang, Michael Y. Sha. Detection of actionable lung cancer fusion genes with known and novel partners from highly degraded FFPE material [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2191.
Abstract 201: Establishment of 3D co-culture spheroid model for in<i>- vitro</i> drug screening
Authors: Christella J. Nelson, Vino T. Cheriyan, Abhishek Pandit, Joseph Francis, Alan Tackett
Journal: Cancer Research (2023)

Abstract Melanoma is an aggressive form of skin cancer that accounts for 75% of deaths of all skin cancers in the United States. Moreover, the number of cases is increasing at an alarming rate than any other cancer worldwide. But what is more alarming is the lack of chemo preventive or therapeutic drugs that are easily accessible to people and the absence of an efficient, effective and reliable model or platform for drug screening. A growing scientific and observational analyses suggests that antioxidants contain in blueberry inhibit tumor growth, and help slow down esophageal, lung, mouth, pharynx, endometrial, pancreatic, prostate, and colon cancers. Lately, the use of 3D multicellular spheroid culture has become a potential link to bridge the gap between monolayer culture and animal model. The treatment of blueberry extract (1mg) on the spheroids of A375 cells showed a disintegration of these spheroids and reduction in their growth. To optimize the culture conditions further herein, we used a novel three-dimensional (3D) coculture system with melanoma (A375), human fibroblast (HF-1) and Human umbilical endothelial cells (HUVECs) to study the effectiveness of drug in vitro. The multicellular nature of the coculture spheroid stimulates the microenvironment of the original tumor which makes it more efficient in drug screening process. The immunofluorescence assay on the 3D spheroid co-culture shows the interactions among these three cells which mimics the tumor microenvironment. We further analyzed the combination of blueberry extract and resveratrol which proved the effectiveness of blueberry extract as a potential chemosensitizer with resveratrol for skin cancer therapy. The complementary effect on the inhibition of A375 cell proliferation were observed when treated with 8 mg blueberry and 10 mM of resveratrol. The results of MTT assay indicates that the blueberry extracts showed potential cytotoxic activity against A375 cell line. 3D spheroid assay and 3D spheroid co-culture assays further confirmed the effectiveness of blueberry and resveratrol combination. Therefore, this platform could be applied for in vitro based drug screening studies. To conclude cytotoxic effects of the blueberry extract in human melanoma cells make them good candidates for further pharmacological studies to discover effective drugs for melanoma therapy. Citation Format: Christella J. Nelson, Vino T. Cheriyan, Abhishek Pandit, Joseph Francis, Alan Tackett. Establishment of 3D co-culture spheroid model for in- vitro drug screening [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 201.
Abstract 1900: Radiotherapy-induced early adverse skin reactions: Comparative analysis of clinician- and patient-reported outcomes in a multi-racial/ethnic breast cancer population (WF-97609)
Authors: James J. Urbanic, Edward G. Shaw, Cristiane Takita, Jean L. Wright, Edward H. Ip, Lingyi Lu, Luis Baez-Diaz, Doris R. Brown, Jon Strasser, Kathy Baglan, Mark Palmer, Anu Thakrar, Amarinthia E. Curtis, Glenn Lesser, Jennifer J. Hu
Journal: Cancer Research (2023)

Abstract Background: Adjuvant radiotherapy (RT) following surgery significantly improves breast cancer survival. However, some patients, particularly minorities, develop early adverse skin reactions (EASRs) or skin toxicities that negatively impact the quality of life (QOL). We assess RT-related EASRs and QOL using clinician-reported outcomes (CROs) and patient-reported outcomes (PROs) in a large multi-racial/ethnic breast cancer population. Methods: This prospective study recruited 1,000 breast cancer patients undergoing RT through the Wake Forest NCI Community Oncology Research Program (NCORP) Research Base between 2011 and 2013. We used the Oncology Nursing Society (ONS) Skin Toxicity Criteria for CROs and Skindex-16 (SD-16) for PROs. Results: This study included 405 non-Hispanic whites (NHW), 277 black/African Americans (AA), 241 HW, 62 Asian/Pacific Islanders (ASPI), and 15 others. About 42% and 15% of patients developed RT-induced ONS grade 3+ and 4+ skin toxicities, respectively. RT-induced EASRs differed significantly by race/ethnicity at mid-RT, 1-month, and 2-month post-RT, but not at the end of RT. Total SD-16 scores differ by race/ethnicity at pre-RT, 1-month, and 6-month post-RT, but not at the end of RT. Overall, PROs have a moderate but significant correlation with CROs at the end of RT. Conclusion: RT-induced EASRs differed significantly by race/ethnicity. There was a moderate but significant correlation between PROs and CROs. However, PROs delineated a broader spectrum in capturing the impact of RT on patients’ QOL, which highlights the importance of integrating PROs in accessing RT-induced EASRs, particularly in minorities with worse RT-induced EASRs. Trial Registration: NCT01407770 (09/02/2011) Citation Format: James J. Urbanic, Edward G. Shaw, Cristiane Takita, Jean L. Wright, Edward H. Ip, Lingyi Lu, Luis Baez-Diaz, Doris R. Brown, Jon Strasser, Kathy Baglan, Mark Palmer, Anu Thakrar, Amarinthia E. Curtis, Glenn Lesser, Jennifer J. Hu. Radiotherapy-induced early adverse skin reactions: Comparative analysis of clinician- and patient-reported outcomes in a multi-racial/ethnic breast cancer population (WF-97609) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1900.
Abstract 190: Personalized identification of cancer treatments in real-time: TumOC - a tumor organoid-on-chip platform for online cell vitality measurements
Authors: Marie Flechner, Juergen Loskutov, Madeleine Nadolny, Ulrike Pfohl, Christian R. Regenbrecht, Katja Uhlig, Lena Wedeken
Journal: Cancer Research (2023)

Abstract Enhanced, physiologically relevant in-vitro tumor models significantly increase the success rate in new drug development, reduce the number of animal experiments and result finally in better therapies for cancer patients. Furthermore, they have the potential to offer new approaches to personalized oncology. In recent years, 3D cell cultures were established as relevant preclinical cancer models, suitable for high-throughput-screening. However, their capacity to model and/or measure physiological processes can still be enhanced. Colorectal carcinomas (CRC) are one of the most common malignant tumors. Due to its heterogeneity and high probability to metastasize, the disease is often incurable and novel, improved therapies are urgently needed. In this project, we developed a tumor organoid-on-chip platform (TumOC) by combining most recent technological advances: We integrated CRC patient-derived 3D cell cultures (organoids) and microsensor particles that enable assessment of cell vitality in real time by measuring oxygen concentration in a microfluidic system. The resulting TumOC platform allows for defined exposition of cytostatic drugs including dynamic and combination treatments. Measurements of cell vitality in real time enables analysis of not only the final effect of a drug treatment, but also the kinetics of drug response. At the same time, utilizing organoids allows for recapitulating tumor architecture and heterogeneity. Using the TumOC platform, we measured the cell vitality in real time over several days during treatment with classic chemotherapeutics or targeted cancer drugs and compared the results to end-point measurements on the same organoids in a static system. We assessed the effect of intra- and intertumoral heterogeneity and developed a protocol for treatment with clinically used combination regimes. In conclusion, our TumOC platform with its ability to recapitulate tumor heterogeneity in combination with dynamic treatments and real-time cell vitality assessment is an in-vitro tumor model closely recapitulating the physiological situation in a patient. TumOC provides an impressive opportunity to test and, consequently, predict the effectiveness of anti-cancer therapies. Therefore, this system is of interest not only for pre-clinical drug development but also for personalized oncology. Citation Format: Marie Flechner, Juergen Loskutov, Madeleine Nadolny, Ulrike Pfohl, Christian R. Regenbrecht, Katja Uhlig, Lena Wedeken. Personalized identification of cancer treatments in real-time: TumOC - a tumor organoid-on-chip platform for online cell vitality measurements [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 190.